AMBER Archive (2006)

Subject: Re: AMBER: Replica Exchange

From: Adrian Roitberg (
Date: Fri Jul 21 2006 - 08:37:26 CDT

Austin B. Yongye wrote:
> Thanks for the response.
> I did contact the author of T-WHAM, but thought some AMBER users might
> have used the code.
> 1. I used REMD because I thought I wasn't getting enough sampling from my
> MD at room temperature.
> 2. Now that I have several trajectories after the REMD, I intend to
> calculate rotamer populations of various dihedral angles in my molecules
> to see if I am getting the correct experimental values. In this paper, J.
> Am. Chem. Soc, 128, 5786-5791 (2006), the authors performed REMD and then
> used T-WHAM for their population distribution analyses at room
> temperature.
> I would like to do similar analysis.
> austin-
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Have you tried to look into the rotamer distribution you are after
without T-WHAM ? I recommend you do that first, do not add a layer of
complication just yet at your level.

So, try to figure out which temperature is the one you want, and look at
that mdcrd as if it was a regular md run (but do not think of it at
time-ordered because it is not).


                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email ============================================================================

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